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WIREs Comput Mol Sci
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Learning from nature: Understanding hydrogenase enzyme using computational approach

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Abstract Learning from nature is a strategy for catalyst development. Its philosophy is that creative designs of high performance catalysts can be obtained from advanced understanding of catalysts selected by nature after billions of years of evolution, such as enzyme. A typical demonstration of such strategy is the developing of catalysts for large‐scale hydrogen production. Hydrogenases due to their impressive performance in catalyzing hydrogen oxidation/production, have been selected as a prototype for human being's learning to achieve better design. Fully understand the structures of hydrogenases and their catalysis mechanisms are essential to reproduce and even outperform this prototype. This article reviews the computational efforts in recent years, focusing on density functional theory calculations on [NiFe] hydrogenases. It summarizes the current knowledge regarding the identification of active sites in [NiFe] hydrogenases and reaction cycles of hydrogen oxidation, followed with a brief collection and discussion of bio‐inspired molecular catalysts derived from [NiFe] hydrogenase model. The capacity of computational calculations for the clarification of catalyst geometries and reaction mechanisms has been highlighted. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Structure and Mechanism > Computational Materials Science Structure and Mechanism > Reaction Mechanisms and Catalysis
Structures of the active sites of the three types of hydrogenases
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Models of the bio‐inspired molecular catalysts
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Different possible paths for the reactivation of Ni‐A and Ni‐B state. The models in the figure are the general view of the structures, which are not necessarily optimized
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Different reaction paths for the whole H2 oxidation process on the active site of [NiFe] hydrogenases. The models in the figure are the general view of these states, which are not necessarily optimized
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Proposed structures of key reaction states in [NiFe] hydrogenases
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Diagram of the H2 oxidation catalytic cycle and deactivation/reactivation mechanism for [NiFe] hydrogenases. The six key states and their relationships are shown in the scheme. H2 oxidation reaction of hydrogenase is marked with bold arrows
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X‐ray crystal structure of the reduced active site of D.v. [NiFe] hydrogenases; the first amino acid shell around the active site has also shown in the figure
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Structure and Mechanism > Reaction Mechanisms and Catalysis
Structure and Mechanism > Computational Materials Science
Structure and Mechanism > Computational Biochemistry and Biophysics

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